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- PDB-3kyo: Crystal structure of HLA-G presenting KLPAQFYIL peptide -

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Basic information

Entry
Database: PDB / ID: 3kyo
TitleCrystal structure of HLA-G presenting KLPAQFYIL peptide
Components
  • Beta-2-microglobulin
  • KLPAQFYIL peptide
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Human leukocyte antigen / major histocompatibility complex / immune response / MHC I
Function / homology
Function and homology information


peripheral B cell tolerance induction / positive regulation of tolerance induction / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / negative regulation of immune response / positive regulation of T cell tolerance induction / negative regulation of G0 to G1 transition / cis-Golgi network membrane ...peripheral B cell tolerance induction / positive regulation of tolerance induction / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / negative regulation of immune response / positive regulation of T cell tolerance induction / negative regulation of G0 to G1 transition / cis-Golgi network membrane / negative regulation of natural killer cell mediated cytotoxicity / filopodium membrane / positive regulation of regulatory T cell differentiation / positive regulation of macrophage cytokine production / protein homotrimerization / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / positive regulation of endothelial cell apoptotic process / cellular defense response / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of angiogenesis / DAP12 interactions / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / early endosome / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / :
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / HLA class I histocompatibility antigen, alpha chain G / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWalpole, N.G. / Rossjohn, J. / Clements, C.S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: The structure and stability of the monomorphic HLA-G are influenced by the nature of the bound peptide
Authors: Walpole, N.G. / Kjer-Nielsen, L. / Kostenko, L. / McCluskey, J. / Brooks, A.G. / Rossjohn, J. / Clements, C.S.
History
DepositionDec 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
P: KLPAQFYIL peptide
Q: KLPAQFYIL peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2658
Polymers89,1476
Non-polymers1182
Water17,889993
1
A: MHC class I antigen
B: Beta-2-microglobulin
P: KLPAQFYIL peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6334
Polymers44,5743
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-19 kcal/mol
Surface area19270 Å2
MethodPISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
Q: KLPAQFYIL peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6334
Polymers44,5743
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-18 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.606, 85.982, 111.570
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MHC class I antigen / HLA-G


Mass: 31601.002 Da / Num. of mol.: 2 / Fragment: residues in UNP 26-298 / Mutation: C66S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-G / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 / References: UniProt: Q9MYA2, UniProt: P17693*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1 / References: UniProt: P61769
#3: Protein/peptide KLPAQFYIL peptide


Mass: 1093.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesised peptide
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 993 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 16% PEG 3350, 0.2M potassium formate, 0.1M HEPES, 10mM cobalt chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→43 Å / Num. obs: 119833 / Rmerge(I) obs: 0.082 / Net I/σ(I): 33.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YDP

1ydp


Resolution: 1.7→43 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.798 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22645 5992 5 %RANDOM
Rwork0.18157 ---
obs0.18382 113595 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.139 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20.57 Å2
2--0.67 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 2 993 7271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0216469
X-RAY DIFFRACTIONr_bond_other_d0.0020.024472
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.9358785
X-RAY DIFFRACTIONr_angle_other_deg1.0093.00210751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36423.371350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.671558
X-RAY DIFFRACTIONr_chiral_restr0.1280.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027271
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021413
X-RAY DIFFRACTIONr_nbd_refined0.2490.21290
X-RAY DIFFRACTIONr_nbd_other0.2310.24735
X-RAY DIFFRACTIONr_nbtor_refined0.1890.23062
X-RAY DIFFRACTIONr_nbtor_other0.0940.23480
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2630.2749
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.255
X-RAY DIFFRACTIONr_mcbond_it3.44434879
X-RAY DIFFRACTIONr_mcbond_other0.76431527
X-RAY DIFFRACTIONr_mcangle_it3.85256171
X-RAY DIFFRACTIONr_scbond_it6.11673164
X-RAY DIFFRACTIONr_scangle_it7.992102611
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 414 -
Rwork0.284 8252 -
obs--97.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.50210.27650.51130.8020.42230.68340.00850.0309-0.02480.0444-0.01690.04870.09270.0420.0084-0.021-0.01790.0014-0.04340.0005-0.005330.58158.208361.1661
20.818-0.0751-0.31323.2246-2.5652.60280.031-0.0084-0.1829-0.1909-0.1868-0.06320.05490.1210.15570.00440.06560.034-0.0310.0572-0.026713.401523.83534.1379
30.6505-0.11670.31020.4642-0.15520.6622-0.0066-0.03230.0087-0.00450.0176-0.06470.10070.0227-0.011-0.01140.0104-0.0039-0.0224-0.008-0.0326-8.29537.548190.3318
40.5665-0.2871-0.54682.24953.00654.10430.00440.005-0.0882-0.00240.0248-0.0224-0.158-0.1323-0.02920.02160.02730.0543-0.0171-0.0089-0.07297.957422.4691117.2071
52.94750.18610.75590.16210.40521.0435-0.05170.1710.23480.0266-0.0017-0.012-0.0022-0.02110.0534-0.0583-0.0122-0.0086-0.02210.07290.01836.838721.172955.5425
62.7425-0.17090.55490.2175-0.3720.8678-0.1133-0.09390.16460.01760.0210.0515-0.00540.02080.0923-0.06180.0031-0.0069-0.0015-0.072-0.004315.289920.393696.4169
73.12034.81324.451911.38097.28116.52830.2213-0.1213-0.18790.3345-0.1393-0.15240.3551-0.0106-0.082-0.0048-0.00180.0027-0.02360.0005-0.034235.8194.633965.1646
81.2023-2.05061.64246.1118-3.92493.87530.16980.20410.0248-0.2622-0.1346-0.00520.33770.1651-0.03510.02020.0042-0.0148-0.0257-0.0167-0.0506-13.52114.15886.2244
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 180
2X-RAY DIFFRACTION2A181 - 274
3X-RAY DIFFRACTION3C2 - 180
4X-RAY DIFFRACTION4C181 - 274
5X-RAY DIFFRACTION5B0 - 99
6X-RAY DIFFRACTION6D0 - 99
7X-RAY DIFFRACTION7P1 - 9
8X-RAY DIFFRACTION8Q1 - 9

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